- recipe cellsnake
cellsnake, a user-friendly tool for single cell RNA sequencing analysis
- Homepage:
- License:
MIT
- Recipe:
- package cellsnake¶
- versions:
0.2.0.12-0,0.2.0.11-2,0.2.0.11-1,0.2.0.11-0,0.2.0-1,0.2.0-0,0.2.0.dev9-0- depends bedtools:
- depends celltypist:
1.3.0- depends cmake:
- depends docopt:
- depends fastp:
- depends fuzzywuzzy:
- depends geos:
3.11.1- depends hdf5:
- depends kraken2:
- depends levenshtein:
- depends matplotlib-base:
<3.7- depends numba:
>=0.56.4- depends openblas:
0.3.21- depends pandas:
<=1.5.3- depends plotly:
- depends pysam:
>=0.16.0.1- depends python:
- depends r-clustree:
0.5.0- depends r-cowplot:
- depends r-curl:
- depends r-dbplyr:
<=2.3.2- depends r-expm:
- depends r-fields:
- depends r-ggalluvial:
- depends r-ggpubr:
- depends r-ggraph:
2.1.0- depends r-ggthemes:
- depends r-gplots:
- depends r-hdf5r:
- depends r-igraph:
- depends r-librarian:
- depends r-matrix:
<=1.5_4.1- depends r-minqa:
- depends r-nmf:
- depends r-openxlsx:
- depends r-optparse:
- depends r-patchwork:
- depends r-plotly:
- depends r-r.utils:
- depends r-randomcolor:
- depends r-reticulate:
- depends r-rsvd:
- depends r-seurat:
4.3.0- depends r-seuratobject:
4.1.3- depends r-spdep:
- depends r-terra:
- depends r-tidyseurat:
- depends r-tidyverse:
- depends r-v8:
- depends r-viridis:
- depends r-xml:
- depends regex:
>=2021.4.4- depends samtools:
- depends scanpy:
1.9.1- depends scipy:
- depends snakemake-minimal:
7.22.0- depends umap-learn:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install cellsnake and update with:: mamba update cellsnake
To create a new environment, run:
mamba create --name myenvname cellsnake
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/cellsnake:<tag> (see `cellsnake/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/cellsnake/README.html)
